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An activating H90 ScFv bound to the hyaluronan-binding domain of human CD44
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H0H experimental model PDB 4PZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100 mM HEPES, 1% PEG 2000 MME, 1 M succinic acid
Crystal Properties Matthews coefficient Solvent content 2.63 53.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.538 α = 90 b = 92.538 β = 90 c = 109.333 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2021-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 56.15 100 0.095 0.097 0.02 1 20.5 44.8 44688
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 100 5.087 5.272 1.354 0.414 0.4 27.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 56.21 44611 2228 99.982 0.196 0.1941 0.2042 0.24 0.2479 RANDOM 45.122
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.271 -1.271 2.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.276 r_dihedral_angle_3_deg 12.489 r_dihedral_angle_2_deg 10.631 r_lrange_other 9.681 r_lrange_it 9.647 r_dihedral_angle_1_deg 7.666 r_scangle_it 6.94 r_scangle_other 6.939 r_mcangle_it 6.3 r_mcangle_other 6.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.276 r_dihedral_angle_3_deg 12.489 r_dihedral_angle_2_deg 10.631 r_lrange_other 9.681 r_lrange_it 9.647 r_dihedral_angle_1_deg 7.666 r_scangle_it 6.94 r_scangle_other 6.939 r_mcangle_it 6.3 r_mcangle_other 6.299 r_scbond_it 4.725 r_scbond_other 4.725 r_mcbond_it 4.363 r_mcbond_other 4.358 r_angle_refined_deg 1.414 r_angle_other_deg 0.496 r_nbd_refined 0.208 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.163 r_xyhbond_nbd_refined 0.16 r_nbd_other 0.135 r_symmetry_nbd_refined 0.11 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.082 r_chiral_restr 0.074 r_metal_ion_refined 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2863 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing